According to Swedish police, witnesses noticed two men running from Strangnas Cathedral before jumping into a small, white speedboat and escaping on Lake Malaren on Tuesday (local time).
Two gold-plated and jewel-encrusted crowns and an orb dating from the 17th-century were reportedly taken.
It sparked a police search of the lake involving boats and helicopters, but they were unable to locate the thieves.
The crowns were part of the funeral regalia of Charles IX, son of Gustav Vasa, who was buried in the cathedral in 1611.
Police could not put a value on the stolen jewels.